Molecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Site (Journal article)

Tatsis, V. A./ Stavrakoudis, A./ Demetropoulos, I. N.

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dc.contributor.authorTatsis, V. A.en
dc.contributor.authorStavrakoudis, A.en
dc.contributor.authorDemetropoulos, I. N.en
dc.date.accessioned2015-11-24T17:04:19Z-
dc.date.available2015-11-24T17:04:19Z-
dc.identifier.issn0301-4622-
dc.identifier.urihttps://olympias.lib.uoi.gr/jspui/handle/123456789/11158-
dc.rightsDefault Licence-
dc.subject*Automationen
dc.subjectBinding Sitesen
dc.subjectPeptides/*chemistryen
dc.subjectStereoisomerismen
dc.subjectTrypsin/*chemistryen
dc.titleMolecular Dynamics as a pattern recognition tool: an automated process detects peptides that preserve the 3D arrangement of Trypsin's Active Siteen
heal.typejournalArticle-
heal.type.enJournal articleen
heal.type.elΆρθρο Περιοδικούel
heal.identifier.primary10.1016/j.bpc.2007.11.008-
heal.identifier.secondaryhttp://www.ncbi.nlm.nih.gov/pubmed/18177993-
heal.languageen-
heal.accesscampus-
heal.recordProviderΠανεπιστήμιο Ιωαννίνων. Σχολή Οικονομικών και Κοινωνικών Επιστημών. Τμήμα Οικονομικών Επιστημώνel
heal.publicationDate2008-
heal.abstractRecently, the synthesis of a molecule has been reported that belongs to a Lysine based, branched cyclic peptide class. This work explores the ability of such molecules to preserve the 3D geometry of the Trypsin's Active Site (TAS) by applying an integrated framework of automated computer procedures. The following four factors a) D/L chirality, b) different amino acids at different positions of the molecular scaffold's cyclic part, c) the application of AMBER and CHARMM force fields and d) different implicit solvation models were evaluated against TAS similarity. It was found that a number of molecules exhibit satisfactory geometric affinity to the TAS during extended Molecular Dynamics runs. We estimated that more than 2000 molecules (belonging to this class) could retain good similarity to the TAS arrangement.en
heal.journalNameBiophys Chemen
heal.journalTypepeer reviewed-
heal.fullTextAvailabilityTRUE-
Appears in Collections:Άρθρα σε επιστημονικά περιοδικά ( Ανοικτά)

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